Update for the delly/call module (#2008)

* updated the delly/call module

* Update modules/delly/call/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/delly/call/main.nf

@@ -8,7 +8,8 @@ process DELLY_CALL {
         'quay.io/biocontainers/delly:1.1.3--h358d541_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(input), path(input_index)
+    path exclude_bed
     path fasta
     path fai
 
@@ -23,13 +24,15 @@ process DELLY_CALL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
     """
     delly \\
         call \\
-        $args \\
+        ${args} \\
-        -o ${prefix}.bcf \\
+        --outfile ${prefix}.bcf \\
-        -g  $fasta \\
+        --genome ${fasta} \\
-        $bam \\
+        ${exclude} \\
+        ${input}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/delly/call/meta.yml

@@ -21,16 +21,26 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
-      description: BAM file from alignment must be sorted, indexed, and duplicate marked
+      description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
-      pattern: "*.{bam}"
+      pattern: "*.{bam,cram}"
+  - bai:
+      type: file
+      description: Index of the BAM/CRAM file
+      pattern: "*.{bai,crai}"
+  - exclude_bed:
+      type: file
+      description: An optional bed file containing regions to exclude from the called VCF
+      pattern: "*.bed"
   - fasta:
       type: file
       description: The reference fasta file
+      pattern: "*.{fasta,fa}"
   - fai:
       type: file
       description: Index of reference fasta file to identify split-reads
+      pattern: "*.fai"
 
 output:
   - meta:
@@ -44,7 +54,7 @@ output:
       pattern: "versions.yml"
   - bcf:
       type: file
-      description: BCF format
+      description: Called variants in BCF format
       pattern: "*.{bcf}"
   - csi:
     type: file
@@ -53,3 +63,4 @@ output:
 
 authors:
   - "@projectoriented"
+  - "@nvnieuwk"

tests/modules/delly/call/main.nf

@@ -10,10 +10,11 @@ workflow test_delly_call_bam {
                     file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
                 ]
 
+    exclude_regions = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
 
-    DELLY_CALL ( input, fasta, fai )
+    DELLY_CALL ( input, exclude_regions, fasta, fai )
 }
 
 workflow test_delly_call_cram {
@@ -22,8 +23,22 @@ workflow test_delly_call_cram {
                     file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
                 ]
 
+    exclude_regions = []
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    DELLY_CALL ( input, fasta, fai )
+    DELLY_CALL ( input, exclude_regions, fasta, fai )
+}
+
+workflow test_delly_call_exclude_regions {
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                ]
+
+    exclude_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DELLY_CALL ( input, exclude_regions, fasta, fai )
 }

tests/modules/delly/call/test.yml

@@ -1,21 +1,32 @@
 - name: delly call test_delly_call_bam
   command: nextflow run ./tests/modules/delly/call -entry test_delly_call_bam -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
   tags:
-    - delly/call
     - delly
+    - delly/call
   files:
     - path: output/delly/test.bcf
-      md5sum: 9d036b140c1bdeab08b7ee6781940fb4
+      md5sum: b5cdb79b69c8254d22fb69173437f9c7
     - path: output/delly/test.bcf.csi
       md5sum: c198abfc14584c5ac69c004057927e0b
 
 - name: delly call test_delly_call_cram
   command: nextflow run ./tests/modules/delly/call -entry test_delly_call_cram -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
   tags:
-    - delly/call
     - delly
+    - delly/call
   files:
     - path: output/delly/test.bcf
-      md5sum: 6c1ec4cfb05ffe9fd93316d2209608ae
+      md5sum: 64980a713438f39d14cffa8458b6a184
+    - path: output/delly/test.bcf.csi
+      md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
+
+- name: delly call test_delly_call_exclude_regions
+  command: nextflow run ./tests/modules/delly/call -entry test_delly_call_exclude_regions -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
+  tags:
+    - delly
+    - delly/call
+  files:
+    - path: output/delly/test.bcf
+      md5sum: 64980a713438f39d14cffa8458b6a184
     - path: output/delly/test.bcf.csi
       md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271